Variant report

Variant	rs3804664
Chromosome Location	chr3:145810408-145810409
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:145810012-145811198	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:145808540..145810799-chr3:145816596..145819414,2	MCF-7	breast:
2	chr3:145809706..145813373-chr3:145877406..145880433,4	MCF-7	breast:
3	chr3:145795852..145797776-chr3:145810151..145811741,2	K562	blood:
4	chr3:145809568..145811317-chr3:145820795..145823225,2	MCF-7	breast:

Variant related genes	Relation type
PLOD2	TF binding region
ENSG00000152952	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs12171294	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12496198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12496358	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12695808	0.90[ASN][1000 genomes]
rs13063887	0.85[ASN][1000 genomes]
rs13088158	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349214	0.90[ASN][1000 genomes]
rs1349215	0.90[ASN][1000 genomes]
rs1355685	0.91[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs1375578	0.81[EUR][1000 genomes]
rs1375581	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375582	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1375584	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1375587	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449438	0.81[EUR][1000 genomes]
rs1449439	0.81[EUR][1000 genomes]
rs1449440	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[ASN][1000 genomes]
rs1449441	0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[ASN][1000 genomes]
rs1449444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449445	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1449450	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1449451	0.86[ASN][1000 genomes]
rs1512900	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1512901	0.85[ASN][1000 genomes]
rs1530741	0.84[ASN][1000 genomes]
rs1562699	0.86[ASN][1000 genomes]
rs1584489	0.81[EUR][1000 genomes]
rs1613698	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs1613796	0.87[ASN][1000 genomes]
rs1707465	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[ASN][1000 genomes]
rs1707466	0.86[ASN][1000 genomes]
rs1707471	0.84[ASN][1000 genomes]
rs1707472	0.84[ASN][1000 genomes]
rs1707473	0.84[ASN][1000 genomes]
rs1707479	0.86[ASN][1000 genomes]
rs1900926	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2029137	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029138	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197908	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2305274	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2669396	0.84[ASN][1000 genomes]
rs2864792	0.91[ASN][1000 genomes]
rs2864793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35399421	0.84[EUR][1000 genomes]
rs3762691	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792339	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs3792341	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804660	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3804661	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3804665	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804666	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804668	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804669	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3804670	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3816399	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3828381	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681111	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681112	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681113	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4681299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6440415	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440417	0.92[ASN][1000 genomes]
rs6440419	0.90[ASN][1000 genomes]
rs6710	0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6770862	0.81[EUR][1000 genomes]
rs6783601	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6799720	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs6800294	0.87[ASN][1000 genomes]
rs6800434	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6801418	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs6802384	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs7431590	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7614409	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[ASN][1000 genomes]
rs7617913	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7639592	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641322	0.88[EUR][1000 genomes]
rs7645622	0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap]
rs764755	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647911	0.80[EUR][1000 genomes]
rs895929	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs895930	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9289712	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9289713	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289714	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9289715	0.83[CEU][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9289716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289717	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289718	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs959329	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963591	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9809099	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9813047	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9822426	0.87[ASN][1000 genomes]
rs9828112	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9836521	0.93[ASN][1000 genomes]
rs9842036	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9842560	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9849076	0.81[EUR][1000 genomes]
rs9852153	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9852725	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858081	0.86[ASN][1000 genomes]
rs9858095	0.87[ASN][1000 genomes]
rs9862005	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862237	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9865802	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9867807	0.81[EUR][1000 genomes]
rs9874388	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874627	0.82[EUR][1000 genomes]
rs9877411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9878166	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9881251	0.93[ASN][1000 genomes]
rs9882583	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877584	chr3:144903957-145833232	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv525829	chr3:145614317-145863779	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv4046	chr3:145693249-145880189	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3804664	PLOD2	cis	parietal	SCAN
rs3804664	PLOD2	cis	Esophagus Mucosa	GTEx
rs3804664	HLTF	cis	parietal	SCAN
rs3804664	PLOD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:145777000-145819400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:145778200-145817200	Weak transcription	Fetal Stomach	stomach
3	chr3:145779600-145820600	Weak transcription	Fetal Kidney	kidney
4	chr3:145780000-145815600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:145780600-145820400	Weak transcription	Placenta	Placenta
6	chr3:145780800-145819800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:145781800-145831800	Weak transcription	Psoas Muscle	Psoas
8	chr3:145782800-145843200	Weak transcription	Pancreas	Pancrea
9	chr3:145784000-145811800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:145784600-145848800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:145785200-145819400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:145789200-145830800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:145789800-145811000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:145790000-145819800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:145790200-145818600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:145790200-145819400	Weak transcription	Left Ventricle	heart
17	chr3:145790400-145843200	Weak transcription	Right Ventricle	heart
18	chr3:145791600-145833800	Weak transcription	NHDF-Ad	bronchial
19	chr3:145792200-145812200	Strong transcription	HSMM	muscle
20	chr3:145794400-145811000	Weak transcription	Adipose Nuclei	Adipose
21	chr3:145794400-145815600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:145794400-145818200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:145794400-145818800	Weak transcription	Ovary	ovary
24	chr3:145794400-145827000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:145794400-145828000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:145794600-145819200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:145796200-145821400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr3:145798000-145818400	Weak transcription	HSMMtube	muscle
29	chr3:145798800-145839200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:145804000-145819200	Weak transcription	NH-A	brain
31	chr3:145804400-145811800	Weak transcription	Fetal Heart	heart
32	chr3:145804600-145818000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:145808000-145810600	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:145808400-145812400	Enhancers	Liver	Liver
35	chr3:145808600-145812000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:145808600-145833000	Weak transcription	Fetal Lung	lung
37	chr3:145808800-145811400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:145809000-145818200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:145809200-145821600	Weak transcription	HMEC	breast
40	chr3:145809600-145817200	Weak transcription	Fetal Intestine Small	intestine
41	chr3:145809800-145812200	Enhancers	A549	lung
42	chr3:145809800-145812200	Enhancers	HepG2	liver
43	chr3:145810000-145810600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:145810000-145810600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:145810000-145810600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:145810000-145810600	Enhancers	Colon Smooth Muscle	Colon
47	chr3:145810000-145811200	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr3:145810200-145810600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:145810200-145812200	Genic enhancers	HUVEC	blood vessel
50	chr3:145810200-145823400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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